To elucidate the effects of temperature and algal cell concentration on pumping of water in the ascidian Ciona intestinalis a number of different experiments were performed. Beat frequency of the lateral cilia in the openings of the branchial sac was measured in intact specimens using a microprojection objective and a monochrome CCD video camera. At constant low algal cell concentration, beat frequencies increased linearly with temperature from 4.0 Hz (±0.5) at 7.4 °C to 13.6 Hz (±1.6) at 20.1 °C. At a constant temperature of 15 °C, beat frequency decreased with increasing algal cell concentration from approximately 3000 to >10 000 Rhodomonas sp. cells ml−1. The decrease was observed both in experiments where the ascidians had been acclimated to a fixed algal cell concentration and in experiments with changing concentrations. Effect of algal cell concentration on squirting/siphon closure and flow velocity in the exhalent siphon was measured using a thermistor. At low algal cell concentrations, flow velocity in the exhalent siphon was stable, apart from a few short squirts. At very high algal cell concentrations, the flow velocity was reduced and much less stable, with prolonged squirting. The effect of gut content on filtration was studied in experiments with specimens acclimated to high algal cell concentrations. Results showed a close relation between gut clearance and filtration rate. From the experimental results and a qualitative analysis of the Ciona-pump it was concluded that the ciliary beat frequency is proportional to the water flow through the sea squirt and that changes in pumping caused by temperature or algal cell concentration are under nervous control or governed by enzyme kinetics, rather than being a result of physico-mechanical properties, i.e. pump efficiency versus flow resistance, of the ascidian pump.